PROBLEM: You have removed the .mobi exporter, and the the new Export > epub > Kindlegen process completely IGNORES the Table of Contents, whether the source anchor option is chosen or not.
Why couldn't you leave it the way it was? It worked great before.
I will be cancelling my CC membership and going back to InDesign 5, which exported .mobi JUST FINE!!
This kind of "improvement" is the most stupid of all.
You're wrong. Adobe never had a mobi export plugin inluded. But several 3rd party developer had some and you might have installed one of them. And you should also consider that Adobe has improved and will improve EPUB export in the future very soon and that there are tons of possibilites to convert EPUB to MOBI.
The link to their plugin page is here.
Unfortunately there is little we can do to help you here as Amazon's InDesign plugin remains in "Beta" and they have not updated it to work on CC, which shipped almost a year ago.
I have had conversations with members of that team about this both in Seattle and in India but whether they do it and when they might do it is entirely upto them.
Do make your interest known over on the Amazon forums here and perhaps they will up their priority for this work.
We too wish KindleGen would more completely support EPUB3 - we intend to keep improving our support as it better captures the design richness that InDesign can create.
Architect, InDesign Engineering